Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Check code style

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/setup-python@v5. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build CCD and wheel for reusing it in several CI jobs

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, actions/setup-python@v5, actions/upload-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Upload CCD to GitHub Releases

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build source distribution

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Test interface to Muscle 5

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, conda-incubator/setup-miniconda@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Test interface to Muscle 5

The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.

Test interfaces to databases and applications

warning libmamba You are using 'pip' as an additional package manager. Be aware that packages installed with 'pip' are managed independently from 'conda-forge' channel.

Test interfaces to databases and applications

warning libmamba [dssp-4.6.1-np2py312h16eb2d3_1] The following files were already present in the environment: - share/libcifpp/components.cif - share/libcifpp/mmcif_ddl.dic - share/libcifpp/mmcif_ma.dic - share/libcifpp/mmcif_pdbx.dic

Test interfaces to databases and applications

warning libmamba [ossuuid-1.6.2-h5888daf_1001] The following files were already present in the environment: - lib/libuuid.a - lib/libuuid.so - lib/pkgconfig/uuid.pc

Test interfaces to databases and applications

The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.

Build documentation

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache/restore@v4, actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, conda-incubator/setup-miniconda@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build documentation

warning libmamba You are using 'pip' as an additional package manager. Be aware that packages installed with 'pip' are managed independently from 'conda-forge' channel.

Build documentation

warning libmamba [ossuuid-1.6.2-h5888daf_1001] The following files were already present in the environment: - lib/libuuid.a - lib/libuuid.so - lib/pkgconfig/uuid.pc

Build documentation

The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.

Build & Test (cp312-macosx_arm64, macos-latest)

Build & Test (cp311-macosx_arm64, macos-latest)

Build & Test (cp314-macosx_arm64, macos-latest)

Build & Test (cp311-win_amd64, windows-latest)

Build & Test (cp312-manylinux_aarch64, ubuntu-24.04-arm)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp314-manylinux_aarch64, ubuntu-24.04-arm)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp313-manylinux_aarch64, ubuntu-24.04-arm)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp311-manylinux_aarch64, ubuntu-24.04-arm)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp312-win_amd64, windows-latest)

Build & Test (cp314-manylinux_x86_64, ubuntu-latest)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp311-manylinux_x86_64, ubuntu-latest)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp312-manylinux_x86_64, ubuntu-latest)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp313-manylinux_x86_64, ubuntu-latest)

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp314-win_amd64, windows-latest)

Build & Test (cp313-macosx_x86_64, macos-latest)

Build & Test (cp313-win_amd64, windows-latest)

Build & Test (cp312-macosx_x86_64, macos-latest)

Build & Test (cp313-macosx_arm64, macos-latest)

Run benchmarks

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/setup-python@v5. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Build & Test (cp311-macosx_x86_64, macos-latest)

Build & Test (cp314-macosx_x86_64, macos-latest)

Artifacts

Produced during runtime

Name	Size	Digest
ccd Expired	36.8 MB	`sha256:105eab511f514f7d45b959058e4d9e5aadb07e218f28267fda7c40d17d8b19b0`
documentation Expired	74.2 MB	`sha256:2747ef8038d19594108c2e9b9d072681fe639f16873d91965d8c9dfe4c54dc54`
internal-build Expired	53.6 MB	`sha256:a2d7204d29926e34e99152820f360d4ae49c256990260f5170569ae3baaa758e`
release-cp311-macosx_arm64 Expired	40.2 MB	`sha256:7151b3b9e886591e40b3e5fe98711bfcd5c5f5bd26c9f37409f8c99c2a1bf3f0`
release-cp311-macosx_x86_64 Expired	40.3 MB	`sha256:70f0685cf1c560025dc850fd16e247db20cabe1563693e7b3763526053e6614b`
release-cp311-manylinux_aarch64 Expired	53.1 MB	`sha256:b468c8d015b09e4f7f7332e04e96fdf7efef2f896a767f696b52fc2188ab330a`
release-cp311-manylinux_x86_64 Expired	53.4 MB	`sha256:14dc73b33565d7074c3856184dedeb9fc0034ca3d2d5029a81d93f6d73ba03c6`
release-cp311-win_amd64 Expired	39.9 MB	`sha256:84f3690a6315cfff5bdd95161d0105611c6c5bdef1c3569265243a9cd9ce3031`
release-cp312-macosx_arm64 Expired	40.1 MB	`sha256:986ca49d33de5bd946e3f3996f34e916ed335a9fe0a87c3434e015b83ac4e3df`
release-cp312-macosx_x86_64 Expired	40.3 MB	`sha256:f99c1cdde40753c717f57a0665306b6aa2bf2ead1396a99f6b9ffd4cb793a2ec`
release-cp312-manylinux_aarch64 Expired	54.3 MB	`sha256:4fc9ed7c44fdb0e4def737ee94ae779b64cb247ce4020aae39a7c7cf931515f5`
release-cp312-manylinux_x86_64 Expired	54.8 MB	`sha256:f19d04bc89a6491552f0b4f6b320e8d13b6a2ce0705b87cf371f88a7cfc0d3fc`
release-cp312-win_amd64 Expired	39.9 MB	`sha256:57c03dbd5ab682b611d65291940922bf6c0de85a1dc8287afa24ee2d0a28f4d2`
release-cp313-macosx_arm64 Expired	40.1 MB	`sha256:440fb9e8c86fbc469a8b895a9ed2fdcf4025808f42e6482943d9a7cbedb8fa45`
release-cp313-macosx_x86_64 Expired	40.3 MB	`sha256:5d6cb24edabcb0d712ecc998c6cb5a5bdf73fe82c191ec04cc2a754e726449d7`
release-cp313-manylinux_aarch64 Expired	54.3 MB	`sha256:fa838a27925399fe6a35e1777813684d6ad19b984caf6eda769be29bbed85220`
release-cp313-manylinux_x86_64 Expired	54.9 MB	`sha256:f1fd9aa8bec31e93e7751d3f043e75a3211cbd61fafa7eb75a3ddf85d132bb42`
release-cp313-win_amd64 Expired	39.9 MB	`sha256:563b013b451eb0a12ed043ea760429d1c9c3ecafdae3cc75130e835860cba2d6`
release-cp314-macosx_arm64 Expired	40.1 MB	`sha256:0d4e5546c7a48f449bb6aa74f986feab274b14019c2c8a723a5bb3f0537895c1`
release-cp314-macosx_x86_64 Expired	40.3 MB	`sha256:d960fd6a3f62af2b28ce920d78dc222445b5909af9013551309cacd65983d964`
release-cp314-manylinux_aarch64 Expired	54.2 MB	`sha256:e376d20c0d5b8a270a3bdc49848f73a848a021c8e004b508a813f5f22b645311`
release-cp314-manylinux_x86_64 Expired	54.6 MB	`sha256:fe405b98c1f729fb7a776c9743698bb119c75f65ff7940596544f7fc24c69103`
release-cp314-win_amd64 Expired	39.8 MB	`sha256:5484c59ff3146967b6bd5bb83e4a5cedb819633cd75fa6c00f5314de082ae4cf`
release-sdist Expired	37.3 MB	`sha256:0a883d8f8b89eabb9ea92befd973210cda31cfd17a614343ca6937490fa11e0b`

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Merge pull request #889 from padix-key/fix-segments #1226

Summary